The present invention relates to a method and to equipment for preparing cheese or a cheese product containing at least one heat-sensitive compound having a positive nutritional effect such as a probiotic bacterium. The preparation method of the invention comprises: hot mixing a cheese paste and at least one compound having a positive nutritional effect, such as a probiotic bacterium, a seric protein, a vitamin or a micronutrient; and hot-metering the mixture thus obtained into a container (10) that is the subsequent packaging of the cheese or cheese product. According to the invention, the mixing is carried out immediately before the metering for a duration lower than 10 seconds and at a temperature higher than or equal to 60°C in order to achieve a minimized thermal spoilage rate of the compound or each compound in said container for the entire product shelf life.